AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053931


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053931.t1 MTR_6g472100 89.160 369 7 3 1 337 1 368 0.0 555
MS.gene053931.t1 MTR_6g046300 93.478 46 1 2 195 240 36 79 3.98e-18 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053931.t1 AT3G25590 33.110 447 134 22 1 320 1 409 7.72e-34 129

Find 53 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGAGGTGGAGCTATATT+TGG 0.183362 5.3:-42493056 MS.gene053931:CDS
GGAGAATTGGGAAACTATTT+AGG 0.222773 5.3:-42493193 MS.gene053931:CDS
TAGAAGAAATCACTTCTTCT+TGG 0.257265 5.3:+42492906 None:intergenic
TTCTTCTATGAATATGAAAA+TGG 0.271087 5.3:-42492891 MS.gene053931:CDS
GGTGGTGGTGGTGGAGGTGA+TGG 0.288439 5.3:-42492663 MS.gene053931:CDS
GCAGATACACTCTCAGCTTT+TGG 0.291697 5.3:-42492726 MS.gene053931:CDS
TTCTTCTTTCTCTTGCATCT+TGG 0.305233 5.3:+42493280 None:intergenic
TTAGAATTAAAATGCTGAAA+TGG 0.330859 5.3:+42493305 None:intergenic
TCAAATATCATTCAAGTTCA+AGG 0.341466 5.3:-42492560 MS.gene053931:CDS
ATTTCTGCAGCTAGAAGTTC+AGG 0.351861 5.3:-42492987 MS.gene053931:CDS
TAGAATTAAAATGCTGAAAT+GGG 0.375136 5.3:+42493306 None:intergenic
CTTGATGCTGGTGGTGGTGG+TGG 0.416125 5.3:-42492675 MS.gene053931:CDS
GGTGGTGGTGGAGGTGATGG+AGG 0.453840 5.3:-42492660 MS.gene053931:CDS
ATCATCATGGAGGTGTTTCA+AGG 0.475029 5.3:-42493097 MS.gene053931:CDS
TAGAAAGAGTACTGGTGTAA+TGG 0.476645 5.3:-42492868 MS.gene053931:CDS
GCAAGAGAAAGAAGAAGAAG+AGG 0.479357 5.3:-42493273 MS.gene053931:CDS
AATAAGAAGAACAAGGATTG+TGG 0.479715 5.3:-42493167 MS.gene053931:CDS
TTGATGGAAGCAGCTACAAT+AGG 0.481008 5.3:-42492842 MS.gene053931:CDS
ACACTTGATGCTGGTGGTGG+TGG 0.488664 5.3:-42492678 MS.gene053931:CDS
GAAAGAAGAAGAAGAGGTTG+TGG 0.494932 5.3:-42493267 MS.gene053931:CDS
GGTGGTTTGATGTTAGAATC+TGG 0.497991 5.3:-42492957 MS.gene053931:CDS
TGAATGAAAGAGGAATTAAG+AGG 0.498145 5.3:-42492620 MS.gene053931:CDS
AACAGAGCATGAATTTCGAT+TGG 0.499202 5.3:+42493388 None:intergenic
ACTGGTGTAATGGAAATTGA+TGG 0.506563 5.3:-42492858 MS.gene053931:CDS
AAAGTATTAAGGGTTGGAGA+TGG 0.524569 5.3:-42492587 MS.gene053931:CDS
GAAAATGGTAGAAAGAGTAC+TGG 0.527029 5.3:-42492876 MS.gene053931:CDS
ATGACACTTGATGCTGGTGG+TGG 0.536535 5.3:-42492681 MS.gene053931:CDS
GTTTGATGTTAGAATCTGGT+AGG 0.549457 5.3:-42492953 MS.gene053931:CDS
AATTTCATGACACTTGATGC+TGG 0.553635 5.3:-42492687 MS.gene053931:CDS
GAATGAAAGAGGAATTAAGA+GGG 0.561877 5.3:-42492619 MS.gene053931:CDS
GCTAGAAGTTCAGGTGTGAA+TGG 0.567727 5.3:-42492978 MS.gene053931:CDS
TTAGAATCTGGTAGGAGAAG+TGG 0.568091 5.3:-42492945 MS.gene053931:CDS
AGATCTCTCTGCAGTTTCAG+AGG 0.571126 5.3:-42493071 MS.gene053931:CDS
AAGGATTGTGGAAGAAGTGT+TGG 0.573763 5.3:-42493155 MS.gene053931:CDS
TCGAAATTCATGCTCTGTTG+AGG 0.575005 5.3:-42493384 MS.gene053931:CDS
GCTATATTTGGATCTGAAGA+TGG 0.581428 5.3:-42493044 MS.gene053931:CDS
ATGTGGATGGTTGATCATCA+TGG 0.586021 5.3:-42493110 MS.gene053931:CDS
TAGGAAGAATAAGAAGAACA+AGG 0.590362 5.3:-42493174 MS.gene053931:CDS
AGGTTCACTATGAATGAAAG+AGG 0.598015 5.3:-42492630 MS.gene053931:CDS
AATTCATGCTCTGTTGAGGT+AGG 0.600288 5.3:-42493380 MS.gene053931:CDS
TTGATGAGAAGAATGAGATG+TGG 0.604022 5.3:-42493127 MS.gene053931:CDS
GAGGTGATGGAGGTTCATGT+AGG 0.609166 5.3:-42492650 MS.gene053931:CDS
TCTCTCTGCAGTTTCAGAGG+TGG 0.611498 5.3:-42493068 MS.gene053931:CDS
TCTGTTGAGGTAGGAAGTGT+TGG 0.616434 5.3:-42493371 MS.gene053931:CDS
AGAAGTTCAGGTGTGAATGG+TGG 0.616507 5.3:-42492975 MS.gene053931:CDS
TGAAGCTTATAGCAATGACA+TGG 0.617179 5.3:-42493579 MS.gene053931:CDS
GTTCAGATTGTGGAGAACAA+AGG 0.625847 5.3:-42493445 MS.gene053931:intron
ATTGTGGAAGAAGTGTTGGT+GGG 0.627755 5.3:-42493151 MS.gene053931:CDS
GATTGTGGAAGAAGTGTTGG+TGG 0.630919 5.3:-42493152 MS.gene053931:CDS
TGAGAAGAATGAGATGTGGA+TGG 0.655301 5.3:-42493123 MS.gene053931:CDS
ATATTTGGATCTGAAGATGG+TGG 0.728625 5.3:-42493041 MS.gene053931:CDS
TTCATGACACTTGATGCTGG+TGG 0.731411 5.3:-42492684 MS.gene053931:CDS
TGGATGGTTGATCATCATGG+AGG 0.776999 5.3:-42493107 MS.gene053931:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGAATTAAAATGCTGAAAT+GGG + chr5.3:42492826-42492845 None:intergenic 20.0%
!! TTAGAATTAAAATGCTGAAA+TGG + chr5.3:42492827-42492846 None:intergenic 20.0%
!! TTATTCATCTGAATCAAAAA+TGG - chr5.3:42493381-42493400 MS.gene053931:CDS 20.0%
!! TTCTTCTATGAATATGAAAA+TGG - chr5.3:42493238-42493257 MS.gene053931:CDS 20.0%
!!! ATATAAAAAGACATGGTTTT+TGG - chr5.3:42492915-42492934 MS.gene053931:CDS 20.0%
!!! ATTTCAGCATTTTAATTCTA+AGG - chr5.3:42492826-42492845 MS.gene053931:CDS 20.0%
!!! GAAAGAAGAAAAAGTATTAA+GGG - chr5.3:42493532-42493551 MS.gene053931:intron 20.0%
!! TCAAATATCATTCAAGTTCA+AGG - chr5.3:42493569-42493588 MS.gene053931:CDS 25.0%
!! TGTGTTGATATAAAAAGACA+TGG - chr5.3:42492908-42492927 MS.gene053931:CDS 25.0%
!!! GGAAAGAAGAAAAAGTATTA+AGG - chr5.3:42493531-42493550 MS.gene053931:intron 25.0%
AATAAGAAGAACAAGGATTG+TGG - chr5.3:42492962-42492981 MS.gene053931:CDS 30.0%
GAATGAAAGAGGAATTAAGA+GGG - chr5.3:42493510-42493529 MS.gene053931:intron 30.0%
TAGAAGAAATCACTTCTTCT+TGG + chr5.3:42493226-42493245 None:intergenic 30.0%
TAGGAAGAATAAGAAGAACA+AGG - chr5.3:42492955-42492974 MS.gene053931:CDS 30.0%
TGAATGAAAGAGGAATTAAG+AGG - chr5.3:42493509-42493528 MS.gene053931:intron 30.0%
TTACTGTCTTAAAGAACGTT+TGG - chr5.3:42492649-42492668 MS.gene053931:CDS 30.0%
! CTAAGAGAGAGTGATTTTAA+AGG - chr5.3:42493322-42493341 MS.gene053931:CDS 30.0%
!! GAAGAAAAAGTATTAAGGGT+TGG - chr5.3:42493536-42493555 MS.gene053931:intron 30.0%
AACAGAGCATGAATTTCGAT+TGG + chr5.3:42492744-42492763 None:intergenic 35.0%
AATTTCATGACACTTGATGC+TGG - chr5.3:42493442-42493461 MS.gene053931:CDS 35.0%
AGGTTCACTATGAATGAAAG+AGG - chr5.3:42493499-42493518 MS.gene053931:intron 35.0%
ATATTTGGATCTGAAGATGG+TGG - chr5.3:42493088-42493107 MS.gene053931:CDS 35.0%
GCTATATTTGGATCTGAAGA+TGG - chr5.3:42493085-42493104 MS.gene053931:CDS 35.0%
GGAGAATTGGGAAACTATTT+AGG - chr5.3:42492936-42492955 MS.gene053931:CDS 35.0%
GTTTGATGTTAGAATCTGGT+AGG - chr5.3:42493176-42493195 MS.gene053931:CDS 35.0%
TGAAGCTTATAGCAATGACA+TGG - chr5.3:42492550-42492569 MS.gene053931:CDS 35.0%
TTCTTCTTTCTCTTGCATCT+TGG + chr5.3:42492852-42492871 None:intergenic 35.0%
TTGATGAGAAGAATGAGATG+TGG - chr5.3:42493002-42493021 MS.gene053931:CDS 35.0%
! AAAGTATTAAGGGTTGGAGA+TGG - chr5.3:42493542-42493561 MS.gene053931:intron 35.0%
! ACTGGTGTAATGGAAATTGA+TGG - chr5.3:42493271-42493290 MS.gene053931:CDS 35.0%
! GAAAATGGTAGAAAGAGTAC+TGG - chr5.3:42493253-42493272 MS.gene053931:CDS 35.0%
!! AGACATGGTTTTTGGAGAAT+TGG - chr5.3:42492923-42492942 MS.gene053931:CDS 35.0%
!! AGAGAGTGATTTTAAAGGCA+TGG - chr5.3:42493327-42493346 MS.gene053931:CDS 35.0%
!! GACATGGTTTTTGGAGAATT+GGG - chr5.3:42492924-42492943 MS.gene053931:CDS 35.0%
!! TAGAAAGAGTACTGGTGTAA+TGG - chr5.3:42493261-42493280 MS.gene053931:CDS 35.0%
AAGCTTGTGTGTTCAGATTG+TGG - chr5.3:42492674-42492693 MS.gene053931:CDS 40.0%
AATTCATGCTCTGTTGAGGT+AGG - chr5.3:42492749-42492768 MS.gene053931:CDS 40.0%
ATGTGGATGGTTGATCATCA+TGG - chr5.3:42493019-42493038 MS.gene053931:CDS 40.0%
ATTTCTGCAGCTAGAAGTTC+AGG - chr5.3:42493142-42493161 MS.gene053931:CDS 40.0%
CATCCTTCTTCTTCTTCTTC+TGG - chr5.3:42492614-42492633 MS.gene053931:CDS 40.0%
GAAAGAAGAAGAAGAGGTTG+TGG - chr5.3:42492862-42492881 MS.gene053931:CDS 40.0%
GAAGAAGGATGCTTCTTACA+TGG + chr5.3:42492605-42492624 None:intergenic 40.0%
GCAAGAGAAAGAAGAAGAAG+AGG - chr5.3:42492856-42492875 MS.gene053931:CDS 40.0%
GGTGGTTTGATGTTAGAATC+TGG - chr5.3:42493172-42493191 MS.gene053931:CDS 40.0%
GTTCAGATTGTGGAGAACAA+AGG - chr5.3:42492684-42492703 MS.gene053931:CDS 40.0%
TCGAAATTCATGCTCTGTTG+AGG - chr5.3:42492745-42492764 MS.gene053931:CDS 40.0%
TGAGAAGAATGAGATGTGGA+TGG - chr5.3:42493006-42493025 MS.gene053931:CDS 40.0%
TTAGAATCTGGTAGGAGAAG+TGG - chr5.3:42493184-42493203 MS.gene053931:CDS 40.0%
TTCAGAGGTGGAGCTATATT+TGG - chr5.3:42493073-42493092 MS.gene053931:CDS 40.0%
TTGATGGAAGCAGCTACAAT+AGG - chr5.3:42493287-42493306 MS.gene053931:CDS 40.0%
! AAGGATTGTGGAAGAAGTGT+TGG - chr5.3:42492974-42492993 MS.gene053931:CDS 40.0%
!! ATCATCATGGAGGTGTTTCA+AGG - chr5.3:42493032-42493051 MS.gene053931:CDS 40.0%
!! ATTGTGGAAGAAGTGTTGGT+GGG - chr5.3:42492978-42492997 MS.gene053931:CDS 40.0%
!! GGTGGTGATTCAGTTTTATC+AGG - chr5.3:42493106-42493125 MS.gene053931:CDS 40.0%
!! TCAGCTTTTGGAAGCATAAG+AGG - chr5.3:42493415-42493434 MS.gene053931:CDS 40.0%
AGAAGTTCAGGTGTGAATGG+TGG - chr5.3:42493154-42493173 MS.gene053931:CDS 45.0%
AGATCTCTCTGCAGTTTCAG+AGG - chr5.3:42493058-42493077 MS.gene053931:CDS 45.0%
CCTCCAGAAGAAGAAGAAGA+AGG + chr5.3:42492620-42492639 None:intergenic 45.0%
CCTTCTTCTTCTTCTTCTGG+AGG - chr5.3:42492617-42492636 MS.gene053931:CDS 45.0%
GCTAGAAGTTCAGGTGTGAA+TGG - chr5.3:42493151-42493170 MS.gene053931:CDS 45.0%
TGGATGGTTGATCATCATGG+AGG - chr5.3:42493022-42493041 MS.gene053931:CDS 45.0%
TTCATGACACTTGATGCTGG+TGG - chr5.3:42493445-42493464 MS.gene053931:intron 45.0%
! GCAGATACACTCTCAGCTTT+TGG - chr5.3:42493403-42493422 MS.gene053931:CDS 45.0%
! TCTGTTGAGGTAGGAAGTGT+TGG - chr5.3:42492758-42492777 MS.gene053931:CDS 45.0%
!! GATTGTGGAAGAAGTGTTGG+TGG - chr5.3:42492977-42492996 MS.gene053931:CDS 45.0%
!! GCTTTTGGAAGCATAAGAGG+TGG - chr5.3:42493418-42493437 MS.gene053931:CDS 45.0%
ATGACACTTGATGCTGGTGG+TGG - chr5.3:42493448-42493467 MS.gene053931:intron 50.0%
TCTCTCTGCAGTTTCAGAGG+TGG - chr5.3:42493061-42493080 MS.gene053931:CDS 50.0%
!! GAGGTGATGGAGGTTCATGT+AGG - chr5.3:42493479-42493498 MS.gene053931:intron 50.0%
!! ACACTTGATGCTGGTGGTGG+TGG - chr5.3:42493451-42493470 MS.gene053931:intron 55.0%
!! CTTGATGCTGGTGGTGGTGG+TGG - chr5.3:42493454-42493473 MS.gene053931:intron 60.0%
!! GATGCTGGTGGTGGTGGTGG+TGG - chr5.3:42493457-42493476 MS.gene053931:intron 65.0%
!! GGTGGTGGTGGAGGTGATGG+AGG - chr5.3:42493469-42493488 MS.gene053931:intron 65.0%
!! GGTGGTGGTGGTGGAGGTGA+TGG - chr5.3:42493466-42493485 MS.gene053931:intron 65.0%
!! GCTGGTGGTGGTGGTGGTGG+AGG - chr5.3:42493460-42493479 MS.gene053931:intron 70.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 42492527 42493624 42492527 ID=MS.gene053931
chr5.3 mRNA 42492527 42493624 42492527 ID=MS.gene053931.t1;Parent=MS.gene053931
chr5.3 exon 42493546 42493624 42493546 ID=MS.gene053931.t1.exon1;Parent=MS.gene053931.t1
chr5.3 CDS 42493546 42493624 42493546 ID=cds.MS.gene053931.t1;Parent=MS.gene053931.t1
chr5.3 exon 42492527 42493461 42492527 ID=MS.gene053931.t1.exon2;Parent=MS.gene053931.t1
chr5.3 CDS 42492527 42493461 42492527 ID=cds.MS.gene053931.t1;Parent=MS.gene053931.t1
Gene Sequence

>MS.gene053931

ATGAAGGAGAAAAACAAAGGTGTTGAAGCTTATAGCAATGACATGGATTGCTACTATTCTACTTCTGATTTTCTTCCATGTAAGAAGCATCCTTCTTCTTCTTCTTCTGGAGGAATATGTGCTTACTGTCTTAAAGAACGTTTGGTCAAGCTTGTGTGTTCAGATTGTGGAGAACAAAGGCTTTCTTCTTGTTCATGCTCTGATGAGATCACTTCCAATCGAAATTCATGCTCTGTTGAGGTAGGAAGTGTTGGAAGAGTCTCATTTCTTATTGAGAATGAAAAGAATGAGACAAACCCATTTCAGCATTTTAATTCTAAGGCCAAGATGCAAGAGAAAGAAGAAGAAGAGGTTGTGGTGCTTAAGAGAAGTAGTAGCAGTTGTGTTGATATAAAAAGACATGGTTTTTGGAGAATTGGGAAACTATTTAGGAAGAATAAGAAGAACAAGGATTGTGGAAGAAGTGTTGGTGGGTTTGATGAGAAGAATGAGATGTGGATGGTTGATCATCATGGAGGTGTTTCAAGGTCAAGATCTCTCTGCAGTTTCAGAGGTGGAGCTATATTTGGATCTGAAGATGGTGGTGATTCAGTTTTATCAGGTGCTAGAAGCTCTATTTCTGCAGCTAGAAGTTCAGGTGTGAATGGTGGTTTGATGTTAGAATCTGGTAGGAGAAGTGGTTACAGTGAAGCTGAACCAAGAAGAAGTGATTTCTTCTATGAATATGAAAATGGTAGAAAGAGTACTGGTGTAATGGAAATTGATGGAAGCAGCTACAATAGGCGTGTGTTTTCACTAAGAGAGAGTGATTTTAAAGGCATGGATGAGTCTAGTTTTATTGATTTGAAGCTTGATTATTCATCTGAATCAAAAATGGCAGATACACTCTCAGCTTTTGGAAGCATAAGAGGTGGAAATTTCATGACACTTGATGCTGGTGGTGGTGGTGGTGGAGGTGATGGAGGTTCATGTAGGTTCACTATGAATGAAAGAGGAATTAAGAGGGAAAGAAGAAAAAGTATTAAGGGTTGGAGATGGATTTTCAAATATCATTCAAGTTCAAGGAAAAGAGATCAAGACCTTATGTTCAAAACCTAA

Protein sequence

>MS.gene053931.t1

MKEKNKGVEAYSNDMDCYYSTSDFLPYCGEQRLSSCSCSDEITSNRNSCSVEVGSVGRVSFLIENEKNETNPFQHFNSKAKMQEKEEEEVVVLKRSSSSCVDIKRHGFWRIGKLFRKNKKNKDCGRSVGGFDEKNEMWMVDHHGGVSRSRSLCSFRGGAIFGSEDGGDSVLSGARSSISAARSSGVNGGLMLESGRRSGYSEAEPRRSDFFYEYENGRKSTGVMEIDGSSYNRRVFSLRESDFKGMDESSFIDLKLDYSSESKMADTLSAFGSIRGGNFMTLDAGGGGGGGDGGSCRFTMNERGIKRERRKSIKGWRWIFKYHSSSRKRDQDLMFKT